[petsc-users] HDF5 DM and VecView with MPI :: Crash

[Thibault Bridel-Bertomeu]

Dear all,

I keep having this error on one of the supercomputers I have access to :

[1]PETSC ERROR: The EXACT line numbers in the error traceback are not
available.

[1]PETSC ERROR: instead the line number of the start of the function is
given.

[1]PETSC ERROR: #1 H5Dcreate2() at
/ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:690

[1]PETSC ERROR: #2 VecView_MPI_HDF5() at
/ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:594

[1]PETSC ERROR: #3 VecView_MPI() at
/ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:787

[1]PETSC ERROR: #4 VecView() at
/ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/interface/vector.c:576

[1]PETSC ERROR: #5 DMPlexCoordinatesView_HDF5_Internal() at
/ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plexhdf5.c:560

[1]PETSC ERROR: #6 DMPlexView_HDF5_Internal() at
/ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plexhdf5.c:802

[1]PETSC ERROR: #7 DMView_Plex() at
/ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plex.c:1366

[1]PETSC ERROR: #8 DMView() at
/ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/interface/dm.c:954

[1]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------

The configure options are as follow :

[1]PETSC ERROR: Configure options --with-clean=1
--prefix=/ccc/work/cont001/ocre/bridelbert/05-PETSC/build_uns3D_inti
--with-make-np=8 --with-windows-graphics=0 --with-debugging=1
--download-mpich-shared=0 --with-x=0 --with-pthread=0 --with-valgrind=0
--PETSC_ARCH=INTI_UNS3D
--with-fc=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpifort
--with-cc=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpicc
--with-cxx=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpicxx
--with-openmp=0
--download-sowing=/ccc/work/cont001/ocre/bridelbert/v1.1.26-p2.tar.gz
--download-metis=/ccc/work/cont001/ocre/bridelbert/git.metis.tar.gz
--download-parmetis=/ccc/work/cont001/ocre/bridelbert/git.parmetis.tar.gz
--download-fblaslapack=/ccc/work/cont001/ocre/bridelbert/git.fblaslapack.tar.gz
--with-cmake-dir=/ccc/products/cmake-3.13.3/system/default
--download-hdf5=/ccc/work/cont001/ocre/bridelbert/hdf5-1.12.0.tar.bz2
--download-netcdf=/ccc/work/cont001/ocre/bridelbert/netcdf-4.5.0.tar.gz
--download-pnetcdf=/ccc/work/cont001/ocre/bridelbert/pnetcdf-1.12.1.tar.gz
--download-exodusii=/ccc/work/cont001/ocre/bridelbert/v2021-01-20.tar.gz
--download-zlib=/ccc/work/cont001/ocre/bridelbert/zlib-1.2.11.tar.gz

The piece of code that is responsible is that one :

                call PetscViewerHDF5Open(PETSC_COMM_WORLD,
"debug_initmesh.h5", FILE_MODE_WRITE, hdf5Viewer, ierr); CHKERRA(ierr)

                call PetscViewerPushFormat(hdf5Viewer,
PETSC_VIEWER_HDF5_XDMF, ierr); CHKERRA(ierr)

                call DMView(dm, hdf5Viewer, ierr); CHKERRA(ierr)

                call PetscViewerPopFormat(hdf5Viewer, ierr); CHKERRA(ierr)

                call PetscViewerDestroy(hdf5Viewer, ierr); CHKERRA(ierr)

I tried with gcc, intel compiler, openmpi 2.x.x or openmpi 4.x.x ... same
problems ... can anyone please advise ? It's starting to make me quite
crazy ... x(

Thank you !!!

Thibault
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